SMTL ID : 7cki.1

Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x 9E0: (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid(Non-covalent)

9E0.1: 17 residues within 4Å: Chain A: F.5, S.6, G.7, I.8, Q.9, V.40, H.43, Q.107, Y.125, M.129, D.132, I.133, V.141, V.143, Q.147 Ligands: MG.2, ATP.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:V.40, A:I.133, A:V.141, A:V.143 Hydrogen bonds: A:Q.107, A:Y.125, A:D.132 Water bridges: A:Q.9, A:Q.9, A:Q.147, A:Q.147 9E0.7: 17 residues within 4Å: Chain B: F.5, S.6, G.7, I.8, Q.9, V.40, H.43, Q.107, Y.125, M.129, D.132, I.133, V.141, V.143, Q.147 Ligands: MG.8, ATP.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.5, B:F.5, B:V.40, B:I.133, B:V.141, B:V.143 Hydrogen bonds: B:Q.107, B:Y.125, B:Y.125, B:D.132, B:D.132 Water bridges: B:Q.9, B:Q.9, B:Q.147, B:Q.147

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.9, K.111 Ligands: 9E0.1, ATP.4 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: Q.9, K.111 Ligands: 9E0.7, ATP.10 No protein-ligand interaction detected (PLIP)

6 x K: POTASSIUM ION(Non-covalent)

K.3: 2 residues within 4Å: Chain A: S.11, Q.49 No protein-ligand interaction detected (PLIP) K.5: 2 residues within 4Å: Chain A: P.200, Y.203 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.203, H2O.2, H2O.6 K.6: 4 residues within 4Å: Chain A: K.232, P.236, S.239, N.240 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.236 K.9: 2 residues within 4Å: Chain B: S.11, Q.49 No protein-ligand interaction detected (PLIP) K.11: 2 residues within 4Å: Chain B: P.200, Y.203 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.203, H2O.8, H2O.12 K.12: 4 residues within 4Å: Chain B: K.232, P.236, S.239, N.240 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.236

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 24 residues within 4Å: Chain A: G.7, I.8, Q.9, S.11, G.17, N.18, G.21, A.22, K.111, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193, S.194, K.195, S.196 Ligands: 9E0.1, MG.2 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:Q.9, A:Q.9, A:Q.9, A:S.11, A:N.18, A:G.144, A:D.146, A:I.183, A:K.192, A:M.193, A:M.193, A:K.195, A:S.196, A:S.196 Water bridges: A:Q.9, A:N.18, A:K.111, A:K.111, A:P.142, A:E.145, A:E.145, A:S.194, A:S.194, A:S.196, A:S.196 Salt bridges: A:K.111, A:K.192, A:K.192, A:K.195, A:K.195, A:K.195 ATP.10: 24 residues within 4Å: Chain B: G.7, I.8, Q.9, S.11, G.17, N.18, G.21, A.22, K.111, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193, S.194, K.195, S.196 Ligands: 9E0.7, MG.8 31 PLIP interactions: 31 interactions with chain B Hydrogen bonds: B:Q.9, B:Q.9, B:Q.9, B:S.11, B:N.18, B:G.144, B:D.146, B:I.183, B:K.192, B:M.193, B:M.193, B:K.195, B:S.196, B:S.196 Water bridges: B:Q.9, B:N.18, B:K.111, B:K.111, B:P.142, B:E.145, B:D.146, B:S.194, B:S.194, B:S.196, B:S.196 Salt bridges: B:K.111, B:K.192, B:K.192, B:K.195, B:K.195, B:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, G. et al., Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin and ATP. To Be Published

Release Date

2021-07-21

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tryptophan--tRNA ligase

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